// To be run from pce/casp5/t0161

SetSeed

InfilePrefix 
Include define-score.script

Time

MakeGenericFragmentLibrary
Time


OutFilePrefix decoys/


InFilePrefix 
ReadTemplateAtoms Template.atoms

Include T0161.t2k.undertaker-align.script 
ReadFragmentAlignment T0161.t2k-2track-undertaker.a2m

InfilePrefix	1jaw/
    include read-alignments.under 
InfilePrefix	1lpuA/
    include read-alignments.under 
InfilePrefix	1cksB/
    include read-alignments.under 
InfilePrefix	1rbv/
    include read-alignments.under 
InfilePrefix	1goa/
    include read-alignments.under 
InfilePrefix	1khhA/
    include read-alignments.under 
InfilePrefix	1aep/
    include read-alignments.under 
InfilePrefix	1goc/
    include read-alignments.under 
InfilePrefix	1dawA/
    include read-alignments.under 
InfilePrefix	1rbt/
    include read-alignments.under 


InFilePrefix

//ReadConformPDB decoys/T0161.try1-opt.pdb
//	NameConform T0161.try9-try1

//ReadConformPDB decoys/T0161.try2-opt.pdb
//	NameConform T0161.try9-try2

//ReadConformPDB decoys/T0161.try3-opt.pdb
//	NameConform T0161.try9-try3

//ReadConformPDB decoys/T0161.try4-opt.pdb
//	NameConform T0161.try9-try4

//ReadConformPDB decoys/T0161.try5-opt.pdb
//	NameConform T0161.try9-try5

//ReadConformPDB decoys/T0161.try6-opt.pdb
//	NameFonform T0161.try9-try6

ReadConformPDB decoys/T0161.try7-opt.pdb
    NameFonform T0161.try9-try7
	
	
Time

ReportCost undertaker-try9.rdb

ConformFromSeq	replace // get a random conformation, removing all-zero one
NameConform T0161.rand
Time

//  TryAllAlign shrink 0.4 min_keep_length 5 
//  TryAllAlign shrink 0.4 min_keep_length 5 cumulative
// NameConform T0161.try5-al2
// PrintConformPDB T0161.try5-al2.pdb edges

// TryAllAlign shrink 0. min_keep_length 1 
// TryAllAlign shrink 0. min_keep_length 1 cumulative
// NameConform T0161.try5-al4
// PrintConformPDB T0161.try5-al4.pdb edges

//  TryAllAlign shrink 0.3 min_keep_length 4 
//  TryAllAlign shrink 0.3 min_keep_length 4 cumulative
// NameConform T0161.try5-al6
// PrintConformPDB T0161.try5-al6.pdb edges

// TryAllAlign shrink 0.1 min_keep_length 2 
// TryAllAlign shrink 0.1 min_keep_length 2 cumulative
//  NameConform T0161.try5-al8
//  PrintConformPDB T0161.try5-al8.pdb edges

// TryAllAlign shrink 0.2 min_keep_length 3
// TryAllAlign shrink 0.2 min_keep_length 3 cumulative
//  NameConform T0161.try5-al10
//  PrintConformPDB T0161.try5-al10.pdb edges

//  TryAllAlign shrink 0. min_keep_length 1 
//  TryAllAlign shrink 0. min_keep_length 1 cumulative
//  NameConform T0161.try5-al12
//  PrintConformPDB T0161.try5-al12.pdb edges

CostConform
Time



// The following alignments are not as good as the ones tried above,
// so are not used in getting the starting point.

ReadFragmentAlignment T0161.t2k.frag
InFilePrefix 

OutFilePrefix 
PrintTemplateAtoms Template.atoms
OutFilePrefix decoys/

Time



InitMethodProbs InsertAlignment 1 \
	ClashingRotamer 2 \
	InsertFragment 5 \
	CrossAndInsert 1 \
	TwoFragment 1 \
	InsertSpecificFragment 5 \
	ReduceBreak 1 \
	CloseGap 0.1 \
	OptSubtree 0.05 \
	JiggleSubtree 0.05 \
	ReduceClash 2 \
	ReduceConstraint 1\
	InsertSSBond 0 \
	ImproveSSBond 0

NameConform T0161.try9
OptConform pool_size 40 num_gen 30 gen_size 140 super_iter 10 \
	pdb scwrl_each use_all
NameConform T0161.try9-opt
PrintConformPDB T0161.try9-opt.pdb edges

SCWRLConform
NameConform  T0161.try9-opt-scwrl
PrintConformPDB T0161.try9-opt-scwrl.pdb 

CostConform
Time

quit